Genome-Wide Identification of m6A-Associated Single-Nucleotide Polymorphisms in Colorectal Cancer

• Published in: Pharmacogenomics and personalized medicine 2021-01, Vol.14, p.887-892
• Main Authors: Zhao, Hongying, Jiang, Jinying, Wang, Mingshan, Xuan, Zixue
• Format: Article
• Language: English
• Subjects: Cancer; Chromosomes; Colorectal cancer; Colorectal carcinoma; Datasets; Disease; Gene expression; Genome-wide association studies; genome-wide association study; Genomes; Lung cancer; N6-methyladenosine; Original Research; Pathogenesis; Prostate cancer; Quantitative trait loci; Single-nucleotide polymorphism; Statistical analysis; Tumors
• ISSN: 1178-7066; 1178-7066
• DOI: 10.2147/PGPM.S314373

Background: N6-methyladenosine (m6A)-associated single-nucleotide polymorphisms (SNPs) play important roles in cancers, with previous research suggesting potential associations between m6A-SNPs and cancer. However, the relationship between the genetic determinants of m6A modification and colorectal cancer (CRC) remains unclear. Methods: An integrative method combining raw data and summary statistics of genome-wide association studies with expression quantitative trait loci (eQTL) and differential expression data was applied to screen potential candidate CRC-associated m6A-SNPs. Results: A total of 402 m6A-SNPs were identified as being associated with CRC (p < 0.001), with 98 showing eQTL signals. In particular, three genes were found to harbor CRC-associated m6A-SNPs: rs178184 in NOVA1, rs35782901 in HTR4, and rs60571683 in SLCO1B3. These genes were differentially expressed in at least one publicly available dataset (p < 0.05), with NOVA1 (p = 3.41× 10− 11) and HTR4 (p = 5.56× 10− 7) being significantly downregulated in CRC (dataset: GSE89076), and SLCO1B3 was significantly overexpressed (datasets: GSE32323 [p = 3.27× 10− 5], GSE21510 [p = 1.09× 10− 6], and GSE89076 [p = 7.63× 10− 6]). Conclusion: This study identified three m6A-SNPs (rs178184, rs35782901, and rs60571683) that may be associated with CRC. However, the lack of analysis of primary CRC samples in order to further elucidate the underlying pathogenesis is a major limitation of this study. Future investigations are needed to validate these CRC-associated m6A-SNPs and explore the m6A-mediated pathogenic mechanism in CRC.